plan_executor 1.0.2 → 1.8.0

data/lib/tests/testscripts/scripts/spec/testscript-example.xml

@@ -0,0 +1,228 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<TestScript xmlns="http://hl7.org/fhir">
+	<id value="testscript-example"/>
+
+	<url value="http://hl7.org/fhir/TestScript/testscript-example"/>
+	<identifier>
+		<system value="urn:ietf:rfc:3986"/>
+		<value value="urn:oid:1.3.6.1.4.1.21367.2005.3.7.9876"/>
+	</identifier>
+	<version value="1.0"/>
+	<name value="TestScript Example"/>
+	<status value="draft"/>
+	<experimental value="true"/>
+	<publisher value="HL7"/>
+	<contact>
+		<name value="Support"/>
+		<telecom>
+			<system value="email"/>
+			<value value="support@HL7.org"/>
+			<use value="work"/>
+		</telecom>
+	</contact>
+	<date value="2016-09-26"/>
+	<description value="TestScript example resource with setup to delete if present and create a new instance of a Patient; and single test definition to read the created Patient with various asserts."/>
+	<jurisdiction>
+		<coding>
+			<system value="urn:iso:std:iso:3166"/>
+			<code value="US"/>
+			<display value="United States of America (the)"/>
+		</coding>
+	</jurisdiction>
+	<purpose value="Patient Conditional Create (Update), Read and Delete Operations"/>
+	<copyright value="© HL7.org 2011+"/>
+
+	<metadata>
+		<capability>
+			<required value="true"/>
+			<description value="Patient Update, Read and Delete Operations"/>
+			<link value="http://hl7.org/fhir/http.html#delete"/>
+			<link value="http://hl7.org/fhir/http.html#read"/>
+			<link value="http://hl7.org/fhir/http.html#update"/>
+			<link value="http://hl7.org/fhir/patient.html"/>
+			<capabilities>
+				<reference value="CapabilityStatement/example" />
+			</capabilities>
+		</capability>
+	</metadata>
+
+	<fixture id="fixture-patient-create">
+		<autocreate value="false"/>
+		<autodelete value="false"/>
+		<resource>
+			<reference value="./_reference/resources/patient-example.json"/>
+			<display value="Peter Chalmers"/>
+		</resource>
+	</fixture>
+
+	<fixture id="fixture-patient-minimum">
+		<autocreate value="false"/>
+		<autodelete value="false"/>
+		<resource>
+			<reference value="./_reference/resources/patient-example.json"/>
+			<display value="Peter Chalmers (minimum)"/>
+		</resource>
+	</fixture>
+
+	<profile id="patient-profile">
+		<reference value="http://hl7.org/fhir/StructureDefinition/Patient" />
+	</profile>
+
+	<variable>
+		<name value="createResourceId"/>
+		<path value="Patient/id"/>
+		<sourceId value="fixture-patient-create"/>
+	</variable>
+
+	<setup>
+		<action>
+			<operation>
+				<type>
+					<system value="http://hl7.org/fhir/testscript-operation-codes"/>
+					<code value="delete"/>
+				</type>
+				<resource value="Patient"/>
+				<label value="SetupDeletePatient"/>
+				<description value="Execute a delete operation to insure the patient does not exist on the server."/>
+				<accept value="json"/>
+				<params value="/${createResourceId}"/>
+			</operation>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned HTTP status is 200(OK) or 204(No Content)."/>
+				<direction value="response"/>
+				<operator value="in"/>
+				<responseCode value="200,204,400,404"/>
+			</assert>
+		</action>
+
+		<action>
+			<operation>
+				<type>
+					<system value="http://hl7.org/fhir/testscript-operation-codes"/>
+					<code value="create"/>
+				</type>
+				<resource value="Patient"/>
+				<label value="SetupCreatePatient"/>
+				<description value="Create patient resource on test server using the contents of fixture-patient-create"/>
+				<accept value="json"/>
+				<contentType value="json"/>
+				<params value="/${createResourceId}"/>
+				<sourceId value="fixture-patient-create"/>
+			</operation>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned HTTP status is 201(Created)."/>
+				<direction value="response"/>
+				<operator value="in"/>
+				<responseCode value="200,201"/>
+			</assert>
+		</action>
+	</setup>
+
+	<test id="01-ReadPatient">
+		<name value="Read Patient"/>
+		<description value="Read a Patient and validate response."/>
+		<action>
+			<operation>
+				<type>
+					<system value="http://hl7.org/fhir/testscript-operation-codes"/>
+					<code value="read"/>
+				</type>
+				<resource value="Patient"/>
+				<description value="Read the patient resource on the test server using the id from fixture-patient-create. Prevent URL encoding of the request."/>
+				<encodeRequestUrl value="false"/>
+				<responseId value="fixture-patient-read"/>
+				<targetId value="fixture-patient-create"/>
+			</operation>
+		</action>
+		<action>
+			<assert>
+				<label value="01-ReadPatientOK"/>
+				<description value="Confirm that the returned HTTP status is 200(OK)."/>
+				<direction value="response"/>
+				<response value="okay"/>
+			</assert>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned HTTP Header Last-Modified is present. Warning only as the server may not support versioning."/>
+				<direction value="response"/>
+				<headerField value="Last-Modified"/>
+				<operator value="notEmpty"/>
+				<warningOnly value="true"/>
+			</assert>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned resource type is Patient."/>
+				<resource value="Patient"/>
+			</assert>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned Patient conforms to the base FHIR specification."/>
+				<validateProfileId value="patient-profile"/>
+			</assert>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned Patient contains the expected family name 'Chalmers'. Uses explicit sourceId reference to read responseId fixture."/>
+				<operator value="equals"/>
+				<path value="fhir:Patient/fhir:name/fhir:family/@value"/>
+				<sourceId value="fixture-patient-read"/>
+				<value value="Chalmers"/>
+			</assert>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned Patient contains the expected given name 'Peter'. Uses explicit sourceId reference to read responseId fixture."/>
+				<operator value="equals"/>
+				<path value="fhir:Patient/fhir:name/fhir:given/@value"/>
+				<sourceId value="fixture-patient-read"/>
+				<value value="Peter"/>
+			</assert>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned Patient contains the expected family name 'Chalmers'. Uses explicit compareToSourceId reference to fixture-patient-create used to create the Patient and implicit reference to read response payload."/>
+				<compareToSourceId value="fixture-patient-create"/>
+				<compareToSourcePath value="fhir:Patient/fhir:name/fhir:family/@value"/>
+				<operator value="equals"/>
+				<path value="fhir:Patient/fhir:name/fhir:family/@value"/>
+			</assert>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned Patient contains the expected family name 'Chalmers'. Uses explicit compareToSourceId reference to fixture-patient-create used to create the Patient and explicit reference to read response payload and default operator of 'equals'."/>
+				<compareToSourceId value="fixture-patient-create"/>
+				<compareToSourcePath value="fhir:Patient/fhir:name/fhir:given/@value"/>
+				<path value="fhir:Patient/fhir:name/fhir:given/@value"/>
+				<sourceId value="fixture-patient-read"/>
+			</assert>
+		</action>
+		<action>
+			<assert>
+				<description value="Confirm that the returned resource contains the expected retained elements and values. Warning only to provide users with reviewable results."/>
+				<minimumId value="fixture-patient-minimum"/>
+				<warningOnly value="true"/>
+			</assert>
+		</action>
+	</test>
+
+	<teardown>
+		<action>
+			<operation>
+				<type>
+					<system value="http://hl7.org/fhir/testscript-operation-codes"/>
+					<code value="delete"/>
+				</type>
+				<resource value="Patient"/>
+				<description value="Delete the patient resource on the test server using the id from fixture-patient-create."/>
+				<targetId value="fixture-patient-create"/>
+			</operation>
+		</action>
+	</teardown>
+</TestScript>

data/lib/tests/testscripts/testscript_engine.rb

@@ -16,15 +16,23 @@ module Crucible
       end
 
       def find_test(key)
-        @scripts.find{|s| s.id == key || s.title == key} || []
+        @scripts.find{|s| s.id == key || s.title == key}
       end
 
       def execute_all
         results = {}
         self.tests.each do |test|
-          # TODO: Do we want to separate out multiserver tests?
-          next if test.multiserver
-          results.merge! test.execute
+          if test.multiserver
+            puts "Skipping Multiserver TestScript: #{test.id}"
+            FHIR.logger.info "Skipping Multiserver TestScript: #{test.id}"
+          elsif test.containsRuleAssertions?
+            puts "Skipping TestScript with permanently-unsupported Rule/RuleSet Assertions: #{test.id}"
+            FHIR.logger.info "Skipping TestScript with permanently-unsupported Rule/RuleSet Assertions: #{test.id}"            
+          else
+            puts "Executing: #{test.id}"
+            FHIR.logger.info "Executing: #{test.id}"
+            results.merge! test.execute
+          end
         end
         results
       end
@@ -39,7 +47,7 @@ module Crucible
             test_metadata = test.collect_metadata(true)
             BaseTest::METADATA_FIELDS.each do |field|
               field_hash = {}
-              test_metadata.each { |tm| field_hash[tm[:test_method]] = tm[field] }
+              test_metadata.values.first.each { |tm| field_hash[tm[:test_method]] = tm[field] }
               list[test.title][field] = field_hash
             end
           end
@@ -54,28 +62,34 @@ module Crucible
         end
       end
 
-      def self.parse_testscript_xml
+      def self.parse_testscripts
         return unless @@models.empty?
-        # get all TestScript's in testscripts/xml
+        # get all specification example TestScripts
         root = File.expand_path '.', File.dirname(File.absolute_path(__FILE__))
-        files = File.join(root, 'xml', '**/*.xml')
-        Dir.glob(files).each do |f|
-          next if f.include? "/_reference/" # to support connectathon11 fixtures; review if there is a better way
-          next if f.include? "Track11-SDC" # uses STU3 models
-          next if f.include? "Track3-CDS-on-FHIR" # uses STU3 models
-          next if f.include? "Track9-Patch" # uses Patch
-          next if f.include? "Track6-FHIR-Genomics" # uses STU3 models
-
-          #TODO: these can be finished with DSTU2
-          next if f.include? "Track2-Terminology"
-          next if f.include? "Track7-LabOrderLabReport"
+        path = File.join(root, 'scripts', 'spec', '**/*.xml')
+        script_files = Dir.glob(path)
+        # get all the Connectathon TestScripts
+        path = File.join(root, 'scripts', 'connectathon', '**/*.xml')
+        script_files += Dir.glob(path)
 
-          @@models << FHIR::TestScript.from_xml( File.read(f) )
+        script_files.each do |f|
+          begin
+            script = FHIR.from_contents( File.read(f) )
+            if script.is_a?(FHIR::TestScript) && script.is_valid?
+              script.url = f # replace the URL with the local file path so file system references can properly resolve
+              @@models << script
+              FHIR.logger.info "TestScriptEngine.parse_testscripts: Loaded #{f}"
+            elsif script.is_a?(FHIR::TestScript)
+              FHIR.logger.error "TestScriptEngine.parse_testscripts: Skipping invalid TestScript #{f}"
+            else # this is a fixture...
+              FHIR.logger.warn "TestScriptEngine.parse_testscripts: Skipping fixture #{f}"
+            end
+          rescue
+            FHIR.logger.error "TestScriptEngine.parse_testscripts: Exception deserializing TestScript #{f}"
+          end
         end
       end
-
     end
-
   end
 end
-Crucible::Tests::TestScriptEngine.parse_testscript_xml
+Crucible::Tests::TestScriptEngine.parse_testscripts

data/plan_executor.gemspec

@@ -4,11 +4,19 @@ Gem::Specification.new do |s|
   s.name = "plan_executor"
   s.summary = "A Gem for handling FHIR test executions"
   s.description = "A Gem for handling FHIR test executions"
-  s.email = "aquina@mitre.org"
+  s.email = "jwalonoski@mitre.org"
   s.homepage = "https://github.com/hl7-fhir/fhir-svn"
-  s.authors = ["Andre Quina", "Jason Walonoski", "Janoo Fernandes", "Michael O'Keefe", "Robert Scanlon"]
-  s.version = '1.0.2'
+  s.authors = ["Andre Quina", "Jason Walonoski", "Janoo Fernandes", "Michael O'Keefe"]
+  s.version = '1.8.0'
   s.license = 'Apache-2.0'
 
   s.files = s.files = `git ls-files`.split("\n")
+
+  s.add_runtime_dependency('nokogiri')
+  s.add_runtime_dependency('nokogiri-diff')
+  s.add_runtime_dependency('fhir_models')
+  s.add_runtime_dependency('fhir_client')
+  s.add_runtime_dependency('ansi')
+  s.add_runtime_dependency('method_source')
+  s.add_runtime_dependency('jsonpath')
 end

data/test/test_helper.rb

@@ -2,7 +2,7 @@ require 'simplecov'
 require_relative '../lib/plan_executor'
 
 require 'pry'
-require 'minitest/autorun'
-require 'bundler/setup'
 require 'test/unit'
-require 'turn'
+require 'bundler/setup'
+
+FHIR.logger.level = Logger::ERROR

data/test/unit/fixtures_test.rb

@@ -2,44 +2,44 @@ require_relative '../test_helper'
 
 class FixturesTest < Test::Unit::TestCase
 
-  fixtures = File.join('fixtures','**','*.xml')
-
-  loading = true
-  t = Thread.new { FHIR::StructureDefinition.load_definitions; loading = false }
+  ERROR_DIR = File.join('tmp', 'errors', 'FixturesTest')
+  # Create a blank folder for the errors
+  FileUtils.rm_rf(ERROR_DIR) if File.directory?(ERROR_DIR)
+  FileUtils.mkdir_p ERROR_DIR
 
-  print 'Loading StructuredDefinitions'
-  while loading do
-    print '.'
-    sleep(10)
-  end
-  print " done.\n"
+  fixtures = File.join('fixtures','**','*.xml')
+  raise 'No Fixture Files Found' if Dir[fixtures].empty?
 
   # Define test methods to validate example JSON
   Dir.glob(fixtures).each do | file |    
     basename = File.basename(file,'.xml')
+    next if basename.start_with?('ccda')
     xml = File.open(file, 'r:bom|UTF-8', &:read)
 
     define_method("test_fixture_validation_#{basename}") do
-      run_validate(file,xml)
+      run_validate(basename,xml)
     end
   end
 
-  def run_validate(file,xml)
-    assert(file && xml)
-
-    r = FHIR::Resource.from_contents(xml)
-    # assert(r.valid?,"#{r.errors.messages}")
+  def run_validate(fixture,xml)
+    assert(fixture && xml)
 
-    root_element = Nokogiri::XML(xml).root.try(:name)      
-    definition = FHIR::StructureDefinition.get_base_definition(root_element)
-    assert(definition)
+    r = FHIR::Xml.from_xml(xml)
+    assert(!r.nil?,"XML fixture does not deserialize.")
     
-    valid = definition.is_valid?(xml,'XML')
-    assert(valid,"XML fixture does not conform to definition: #{definition.name}")
+    errors = FHIR::Xml.validate(xml)
+    if !errors.empty?
+      File.open("#{ERROR_DIR}/#{fixture}.err", 'w:UTF-8') do |file|
+        file.write "#{fixture}: #{errors.length} errors\n\n"
+        errors.each do |error|
+          file.write(sprintf("%-8d  %s\n", error.line, error.message))
+        end
+      end
+      File.open("#{ERROR_DIR}/#{fixture}.xml", 'w:UTF-8') { |file| file.write(xml) }
+    end
 
-    resource = FHIR::Resource.from_contents(xml)
-    valid = definition.is_valid?(resource)
-    assert(valid,"Resource does not conform to definition: #{definition.name}")    
+    assert(errors.empty?,"XML fixture does not conform to schema.")
+    # TODO Add StructureDefinition validation.
   end
 
 end

data/test/unit/metadata_test.rb

@@ -3,16 +3,16 @@ require_relative '../test_helper'
 class MetadataTest < Test::Unit::TestCase
 
   # Test gathering metadata for all the Suites
-  # def test_suite_list
-  #   metadata = Crucible::Tests::SuiteEngine.list_all(true)
-  #   assert !metadata.blank?, 'Failed to gather SuiteEngine metadata.'
-  # end
+  def test_suite_list
+    metadata = Crucible::Tests::SuiteEngine.list_all(true)
+    assert !metadata.blank?, 'Failed to gather SuiteEngine metadata.'
+  end
 
   # Test gathering metadata for all the TestScripts
-  # def test_testscript_list
-  #   metadata = Crucible::Tests::TestScriptEngine.list_all(true)
-  #   assert !metadata.blank?, 'Failed to gather TestScriptEngine metadata.'
-  # end
+  def test_testscript_list
+    metadata = Crucible::Tests::TestScriptEngine.list_all(true)
+    assert !metadata.blank?, 'Failed to gather TestScriptEngine metadata.'
+  end
 
   # Test gathering metadata for all the tests via the Executor
   def test_executor_list
@@ -26,8 +26,18 @@ class MetadataTest < Test::Unit::TestCase
     read_test = executor.find_test('ReadTest')
     assert !read_test.nil?, 'Could not find ReadTest Suite'
     metadata = executor.extract_metadata_from_test('ReadTest')
-    puts JSON.pretty_generate(metadata)
+    FHIR.logger.debug JSON.pretty_generate(metadata)
     assert !metadata.blank?, 'Failed to retrieve ReadTest Suite metadata'
   end
 
+  def test_testscript_find
+    tests = Crucible::Tests::TestScriptEngine.list_all
+    assert !tests.blank?, "Failed to list testscripts."
+
+    testscript_engine = Crucible::Tests::TestScriptEngine.new(nil)
+
+    keyed_test = testscript_engine.find_test('TS-testscript-example')
+    assert !keyed_test.nil?, "Failed to find testscript by key"
+  end
+
 end